Error loading ArrayExpress in R 2.12 Mac
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@michael-dondrup-3849
Last seen 6.6 years ago
Hi, I am trying to load package ArrayExpress, but: > biocLite("ArrayExpress") Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "ArrayExpress" Please wait... trying URL 'http://www.bioconductor.org/packages/2.7/bioc/bin/macosx/l eopard/contrib/2.12/ArrayExpress_1.10.0.tgz' Content type 'application/x-gzip' length 162415 bytes (158 Kb) opened URL ================================================== downloaded 158 Kb > library(ArrayExpress) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versio ns/2.12/Resources/library/preprocessCore/libs/x86_64/preprocessCore.so ': dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/libra ry/preprocessCore/libs/x86_64/preprocessCore.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.11/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.12/Resou rces/library/preprocessCore/libs/x86_64/preprocessCore.so Reason: image not found Error: package/namespace load failed for 'ArrayExpress' This reminds me to an error reported earlier about the bioconductor MacOS build, but I thought that was fixed. Or is it a missing dependency? Best Michael > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 limma_3.6.0 tools_2.12.0 XML_3.2-0 >
ArrayExpress ArrayExpress • 773 views
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@sean-davis-490
Last seen 4 days ago
United States
On Thu, Oct 21, 2010 at 7:46 AM, Michael Dondrup <michael.dondrup@uni.no>wrote: > Hi, > I am trying to load package ArrayExpress, but: > > > > > biocLite("ArrayExpress") > Using R version 2.12.0, biocinstall version 2.7.4. > Installing Bioconductor version 2.7 packages: > [1] "ArrayExpress" > Please wait... > > trying URL ' > http://www.bioconductor.org/packages/2.7/bioc/bin/macosx/leopard/con trib/2.12/ArrayExpress_1.10.0.tgz > ' > Content type 'application/x-gzip' length 162415 bytes (158 Kb) > opened URL > ================================================== > downloaded 158 Kb > > > > library(ArrayExpress) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/pre processCore/libs/x86_64/preprocessCore.so': > dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/libr ary/preprocessCore/libs/x86_64/preprocessCore.so, > 6): Library not loaded: > /Library/Frameworks/R.framework/Versions/2.11/Resources/lib/libR.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/2.12/Resources/library/prep rocessCore/libs/x86_64/preprocessCore.so > Reason: image not found > Error: package/namespace load failed for 'ArrayExpress' > > This reminds me to an error reported earlier about the bioconductor MacOS > build, but I thought that was fixed. Or is it a missing dependency? > Looks like your preprocessCore package is still affected by the build problems. You could try reinstalling preprocessCore (and potentially other packages that were affected by the build problems) and see if that fixes things. Sean > > Best > Michael > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 limma_3.6.0 tools_2.12.0 XML_3.2-0 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Yes, re-installing preprocessCore fixes it. Strange though, I did a re- install before via biocLite() and biocLite("affy"), maybe that package wasn't re-installed because it was there as a dependency. So I will run biocLite(installed.packages()[,1]) to be on the safe side. Thanks Michael On Oct 21, 2010, at 1:54 PM, Sean Davis wrote: > Looks like your preprocessCore package is still affected by the build problems. You could try reinstalling preprocessCore (and potentially other packages that were affected by the build problems) and see if that fixes things. >
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On Thu, Oct 21, 2010 at 9:04 AM, Michael Dondrup <michael.dondrup@uni.no>wrote: > Yes, > re-installing preprocessCore fixes it. Strange though, I did a re- install > before via biocLite() and biocLite("affy"), maybe that package wasn't > re-installed because it was there as a dependency. I think that was the case, yes. > So I will run biocLite(installed.packages()[,1]) to be on the safe side. > > Thanks > Michael > > > > > On Oct 21, 2010, at 1:54 PM, Sean Davis wrote: > > > Looks like your preprocessCore package is still affected by the build > problems. You could try reinstalling preprocessCore (and potentially other > packages that were affected by the build problems) and see if that fixes > things. > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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